Chapter 1: Introduction to Obelisks

Have you ever come across the term "Obelisks"? Surprisingly, these entities are even tinier than virus particles, yet they possess the remarkable ability to transmit information to larger life forms.

New life forms are rarely discovered, although we frequently identify new species across various organisms. The emergence of an entirely new category of life is particularly infrequent, especially among minuscule entities. It was in 1676 that Antonie van Leeuwenhoek, known as the Father of Microbiology, first observed and described what we now identify as bacteria using microscopes he crafted himself. Remarkably, it took over a century for another scientist to recognize and describe them again. He also documented protozoans, small organisms exhibiting both plant and animal traits, commonly referred to as protists.

So, how many distinct classes of living organisms exist? Before unveiling today's topic, which centers around a newly discovered organism, let's review the biological tree of life. Don’t worry; this isn’t a test!

The tree typically includes five primary categories of life: Viruses, Bacteria, Archaea, Animals, and Plants. Some classification systems also recognize Fungi as a separate class. Taxonomists often have differing opinions, leading to periodic reclassifications, so consider this a well-supported framework rather than a definitive answer. Now, let’s delve into the newly discovered life forms known as Obelisks.

Chapter 2: The Nature of Obelisks

The Obelisks share similarities with what molecular biologists classify as viroid-like particles. To comprehend these new entities, we must first explore the existing viroid-like particles with which they are connected.

To begin, let’s discuss viruses, since the term “viroid-like” implies a resemblance to virus particles. Viruses are categorized into two main types based on their genetic material: those with RNA genomes and those with DNA genomes. They typically range in size from 20 to 300 nanometers. This small size necessitates the use of specialized masks, like N95, to filter out such minuscule particles and prevent infections from viruses such as COVID-19 or Flu.

Viroid-like particles, identified over a decade ago, are small RNA fragments initially observed in plant cells. They are categorized based on their RNA structure, activity, location within host cells, genomic organization, replication methods, and phylogenetic relationships. The focus on these particles stems from their capacity to cause crop losses, prompting farmers to seek preventive measures.

What exactly are Obelisks? The term might not have crossed your mind recently, and I certainly can’t recall the last time I heard it. Interestingly, the word has its roots in Ancient Greek, referring to a tall, four-sided monument tapering to a point. The Washington Monument in D.C. is a well-known example.

Now, do these viroid-like particles resemble the architectural form of an obelisk? That remains uncertain, as no one has yet captured an image of these viroid-like entities.

The journey to discovering these “creatures” began with an interest in the human gut microbiome. Zheludev and colleagues aimed to identify viroid-like and other genetic elements amid the diverse life forms present in our microbiomes. They developed a bioinformatics tool called VNom to locate novel viroid-like elements.

Instead of conducting fresh sampling and sequencing, they utilized data from a comprehensive study of fecal samples from 104 donors collected over a year. This extensive dataset was publicly available, allowing Zheludev’s team to apply their VNom tool effectively. They successfully identified a new class of viroid-like genetic elements, termed Obelisks.

The Obelisks exhibit several notable features: (i) a circular RNA genome of approximately 1kb, (ii) predicted rod-like secondary structures encapsulating the genome, and (iii) open reading frames coding for a novel protein superfamily called "Oblins." These findings position Obelisks as a distinct phylogenetic group, lacking similarity to known biological agents.

To visualize their structure, Zheludev's team used known RNA folding patterns to predict the 3D configuration of these molecules. The first image illustrates the rod-like secondary structures, while the second shows the circular RNA genome comprising 1164 nucleotides.

After identifying the Obelisks, they expanded their search using additional scanning tools across 5.4 million datasets, resulting in the discovery of around 30,000 Obelisks categorized into 15 subtypes based on the number of Oblin proteins and their predicted structures.

The first video titled "The 1100 ton Unfinished Obelisk - Carved with Pounding Stones? An UnchartedX Investigation!" delves into the history and mystery surrounding obelisks, exploring their construction and significance in ancient cultures.

Chapter 3: Reproduction of Obelisks

An intriguing question arises: How do Obelisks reproduce? Similar to viruses, viroid-like particles require a host to replicate. The initial viroid-like entities were found associated with plants, but the Obelisks were identified in a different context. They were isolated from fecal microbiomes, which encompass a variety of microorganisms, including bacteria, yeast, fungi, and other viruses.

Zheludev and his team faced challenges in determining specific host-agent relationships from metagenomic data. The samples containing Obelisk homologues were derived from complex mixtures, making the potential hosts unclear. However, they discovered a correlation between Obelisks and "Streptococcus sanguinis," a commensal bacterium in the healthy human oral microbiome. This is promising, as it suggests that Obelisks are unlikely to pose any pathogenic threats.

As they noted, the strong correlation between S. sanguinis SK36 and the Obelisk RNA-seq reads indicates S. sanguinis SK36 as a potential model for future Obelisk characterization. Future studies will confirm this correlation and may identify additional commensal hosts for the Obelisks.

Chapter 4: Why the Name "Obelisks"?

The designation "Obelisks" stems from the predicted rod-like structure of the RNA strands. Zheludev and colleagues referred to this group as Obelisk-alpha due to the remarkable rod-like secondary structure observed. At 1164 nucleotides in length, this folding contrasts with typical mRNA sequences, which do not readily adopt such shapes.

Despite this naming, I remain skeptical of the comparison. A rod-like structure does not necessarily resemble an obelisk, which has a broad base tapering to a point. However, naming such entities can be challenging, and I invite your thoughts on potential alternatives in the comments!

In summary, the exploration of the Obelisks reveals the vast unknowns within our understanding of life. The study illustrates significant advancements in bioinformatics, enabling the analysis of millions of datasets that would have been unimaginable just a few years ago.

The implications of this discovery extend beyond our current understanding, offering insights into the evolution of life. Zheludev and colleagues propose that Obelisks may not fit neatly into the virus category, suggesting the possibility of a new group of entities that could bridge the gap between simple genetic molecules and complex viruses.

Until next time,

Rich

P.S. If you enjoyed this article, consider exploring these related posts:

• Exploring Frogs With Transparent Skin: Glass frogs allow us to see their internal structures!
• Unraveling Rafflesia: A Unique Parasitic Plant
• Surprising Discoveries of Gigantic Genomes and Salamander Cells

The second video titled "Egypt's Obelisks: Part Of An Ancient Energy System?" investigates the potential energy-related functions of obelisks in ancient Egyptian civilization.